Hello! I just received a stomp shield kit from synthcube, and while putting it together I realized that the kit was missing 2 3.9nF capacitors, and a 15nF capacitor. Is this because the components have been updated since then, or do I really need those capacitors?

you need those capacitors. you should contact synthcube and let them know, there might be an issue with their stuffing operation, and it would be good for them to catch it sooner rather than later. synthcube has taken over stuffing those kits.